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- PDB-5t2t: Crystal structure of Lymphocytic choriomeningitis mammarenavirus ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5t2t | ||||||
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Title | Crystal structure of Lymphocytic choriomeningitis mammarenavirus endonuclease bound to compound L742001 | ||||||
![]() | RNA-directed RNA polymerase L | ||||||
![]() | TRANSFERASE / mammarenavirus / LCMV / endonuclease / inhibitor | ||||||
Function / homology | ![]() RNA-templated viral transcription / negative stranded viral RNA replication / cap snatching / virion component / host cell cytoplasm / Hydrolases; Acting on ester bonds / hydrolase activity / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Saez-Ayala, M. / Yekwa, E.L. / Canard, B. / Alvarez, K. / Ferron, F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structures ofLymphocytic choriomeningitis virusendonuclease domain complexed with diketo-acid ligands. Authors: Saez-Ayala, M. / Yekwa, E.L. / Carcelli, M. / Canard, B. / Alvarez, K. / Ferron, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106.3 KB | Display | ![]() |
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PDB format | ![]() | 80.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5ltfC ![]() 5ltnC ![]() 5ltsC ![]() 3jsbS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 23722.172 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: L, KUE_IGS310002 / Production host: ![]() ![]() References: UniProt: A0A059U382, UniProt: P14240*PLUS, RNA-directed RNA polymerase |
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-Non-polymers , 6 types, 355 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/0N8.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/0N8.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-0N8 / ( | #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.444 Å3/Da / Density % sol: 64.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Na citrate 0,1M, Isopropanol 3,5%, MnCl2 1mM, L742001 2mM |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 9, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8729 Å / Relative weight: 1 |
Reflection | Resolution: 1.967→54.06 Å / Num. obs: 44686 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.998 / Net I/σ(I): 12.51 |
Reflection shell | Resolution: 1.967→2.037 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 2.02 / CC1/2: 0.715 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3JSB Resolution: 1.967→54.058 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.41 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.967→54.058 Å
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Refine LS restraints |
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LS refinement shell |
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